chr20-54899324-C-A

Variant names:

• chr20-54899324-C-A
• rs6069045

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.552 in 152,004 control chromosomes in the GnomAD database, including 25,488 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.55 (25488 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.281
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83845 AN: 151886 Hom.: 25491 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.636

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.732

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.560

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.552 AC: 83846 AN: 152004 Hom.: 25488 Cov.: 32 AF XY: 0.556 AC XY: 41308 AN XY: 74320

African (AFR) AF: 0.292 AC: 12086 AN: 41424

American (AMR) AF: 0.490 AC: 7491 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2540 AN: 3468

East Asian (EAS) AF: 0.470 AC: 2419 AN: 5148

South Asian (SAS) AF: 0.673 AC: 3245 AN: 4824

European-Finnish (FIN) AF: 0.732 AC: 7736 AN: 10570

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.682 AC: 46378 AN: 67976

Other (OTH) AF: 0.556 AC: 1175 AN: 2112

Alfa AF: 0.639 Hom.: 21221

Bravo AF: 0.520

Asia WGS AF: 0.535 AC: 1864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.5
DANN	Benign	0.46
PhyloP100		0.28

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6069045; hg19: chr20-53515863;